I prefer a structure where I organize them by features. The name reflects the rule set they're in (ie Lights-Outdoor-Gate is in Lights-Outdoor) to simplify discoverability, until a global search is added 
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Organizing/ structuring rule sets and rules -
Organizing/ structuring rule sets and rulesI do a mix. I have rule sets for each room. Generally, these manage lighting, and maybe a small number of specific devices in that area. I have functional rule sets for other things like determining house mode (which is really a blend of season, day of week, time of day, and other switches I can throw for when we're having a party or overnight guests). Functional rule sets also cover room- or level-spanning rules. For example, I bring management of all leak detectors to a single utility rule set.
There's no harm in moving things around. Rules in rule sets have unique IDs that are not affected by their parent location, so moving them changes nothing operationally, it's just an organizational tool for the user. Make a structure and evolve it as you find need. You'll settle into something that works for you.
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Moving MSR from a QNAP container to RP 5 - some issuesI know I sound like a broken record, but look at the logs. At startup, much is logged, and if there are problems with file permissions (which I suspect), you'll see it mentioned there in some form.
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Moving MSR from a QNAP container to RP 5 - some issues
